A cross-disciplinary partnership between epigenetics researchers at the Babraham Institute and physicists at the Cavendish Laboratory at the University of Cambridge has shown that cell-to-cell variability in DNA methylation in mouse embryonic stem cells is explained by oscillations in DNA methylation occurring within each cell. Unpicking the complexity of what drives and defines cellular identity is essential for future healthcare revolutions such as the use of adult stem cells in therapy approaches as well as epigenetic-based treatments for cancer. The research findings are published today in the journal Cell Systems.

Embryonic stem cells, the early unspecified cells of the embryo, are pluripotent – meaning that they are capable of becoming any cell in the body. They are also classified as either naïve or primed; primed cells are developmentally a step closer to committing to specific cell lineages. DNA methylation – additions of small chemical markers to the DNA – is needed for primed stem cells to exit the pluripotent state and to develop into one of the many cell types present in the fully formed embryo.

Surprisingly, previous research has shown that a freeze-frame snapshot of primed mouse embryonic stem cells reveals highly variable amounts of DNA methylation. This latest research used quantitative single-cell sequencing methods to measure this variability, finding that genome-wide DNA methylation ranged from 17-86%. The researchers then developed this analysis further, adding a time course analysis tracking synchronised cells and identified a robust cycle of DNA methylation oscillations.

Joint first author, Dr Heather Lee, undertook the epigenetics analysis for this work as a postdoctoral researcher at the Babraham Institute and is now an independent group leader at the University of Newcastle in Australia. She explains: “Our study shows that DNA methylation is incredibly variable in pluripotent cells. Amazingly, this variability was not restricted to specific parts of the genetic material, but was observed on a genome-wide scale. Furthermore, we could eliminate this variability by interfering with the processes that add and remove DNA methylation, demonstrating a link to rapid turnover of DNA methylation.

“This plasticity may allow pluripotent cells to explore their options before committing to a differentiation pathway.

“Our findings point to the power of single-cell analysis. We would never have suspected these oscillations by looking at combined cell populations.”

Combining single-cell techniques with biophysical modelling allowed the researchers to model the production and turnover of DNA methylation by the main enzymes involved to see if these parameters could be responsible for generating the oscillation patterns seen in the cells. Dr Steffen Rulands, joint first author on the paper from his time as postdoctoral researcher at the Cavendish Laboratory and now an independent group leader at the Max Planck Institute for the Physics of Complex Systems in Dresden, Germany, commented: “Using methods from theoretical physics we were able to unveil the dynamical rules that govern DNA methylation from the static information provided by single-cell sequencing experiments.”

Professor Ben Simons, Herchel Smith Professor of Physics at the Cavendish Laboratory, University of Cambridge, continued: “This study presents a vivid illustration of how concepts from statistical physics and dynamical systems can reveal, and provide mechanistic insight into, cooperative phenomena in biological systems, even at the subcellular scale. Moving forward, it will be exciting to discover whether similar conceptual approaches may help to understand how dynamic changes in DNA methylation influence cell fate decision-making during development and in diseased states.”

Looking forward, the Institute’s strength in single-cell analyses and ongoing collaborations with the Simons and Rulands labs will help confirm the link between the DNA methylation oscillations and associated variation in gene expression suggested by this research.

Professor Wolf Reik, Head of the Epigenetics research programme at the Babraham Institute, said: “The rapid cycling of DNA methylation in embryonic stem cells is an intriguing discovery and we’re still pondering what this might mean in biological terms.

"Our research aims to discover how stem cells are directed into becoming the different cells of our bodies. Epigenetics is as the heart of this process. Thinking of situations where this cell identity is lost, such as the loss of cell identity in cancer and other diseases, it’s possible that this could occur through this type of mechanism affecting the epigenetic state of those cells.”

Research funding
This work received funding from a variety of research funders to each participating group: BBSRC, the Wellcome Trust, EMBL, the EU and MRC. Please see the paper for details of individual funding sources. The Babraham Institute receives strategic funding from the Biotechnology and Biological Sciences Research Council (BBSRC).

Image
Differences in DNA methylation levels in a population of mouse embryonic stem cells grown in serum (primed). The signal intensity of staining for DNA methylation was converted to a heat map showing high signal in red and low signal in blue. Image: Dr Fátima Santos and Dr Wendy Dean, Babraham Institute.

Animal statement
As a publicly funded research institute, the Babraham Institute is committed to engagement and transparency in all aspects of its research. Animals are only used in Babraham Institute research when their use is essential to address a specific scientific goal, which cannot be studied through other means. The main species used are laboratory strains of rodents, with limited numbers of other species. We do not house cats, dogs, horses or primates at the Babraham Research Campus for research purposes.

This research used embryonic stem cells obtained from mice embryos at different stages of development. Embryonic stem cells were collected from the embryos after the pregnant mouse was humanely killed. Please follow the link for further details of the Institute’s animal research and our animal welfare practices.

About the Babraham Institute
The Babraham Institute undertakes world-class life sciences research to generate new knowledge of biological mechanisms underpinning ageing, development and the maintenance of health. Our research focuses on cellular signalling, gene regulation and the impact of epigenetic regulation at different stages of life. By determining how the body reacts to dietary and environmental stimuli and manages microbial and viral interactions, we aim to improve wellbeing and support healthier ageing. The Institute receives core funding from the Biotechnology and Biological Sciences Research Council (BBSRC) through an Institute Core Capability Grant.

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